Domain-aware priors stabilize, not merely enable, vertical federated learning in data-scarce coral multi-omics

Sam Victor

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arXiv · 2601.00050

Domain-aware priors stabilize, not merely enable, vertical federated learning in data-scarce coral multi-omics

Sam Victor

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Abstract

Vertical federated learning (VFL) enables multi-laboratory collaboration on distributed multi-omics datasets without sharing raw data, but exhibits severe instability under extreme data scarcity (P >> N) when applied generically. Here, we investigate how domain-aware design choices; specifically gradient saliency-guided feature selection with biologically motivated priors; affect the stability, interpretability, and failure modes of VFL architectures in small-sample coral stress classification (N = 13 samples, P = 90,579 features across transcriptomics, proteomics, metabolomics, and microbiome data). We benchmark REEF (Robust Expert Encoder Federation), a domain-aware VFL framework, against two baselines on the Montipora capitata thermal stress dataset: (i) a standard NVFlare-based VFL and (ii) LASER, a state-of-the-art label-aware VFL method. REEF achieves an AUROC of 0.776 +/- 0.039 after reducing dimensionality by 98.6% (90,579 to 1,300 features), substantially outperforming NVFlare VFL at chance level (AUROC 0.500 +/- 0.125, p = 0.0106, Cohen's d = 2.265) and numerically exceeding LASER (AUROC 0.557 +/- 0.191, p = 0.0995, Cohen's d = 1.068), with 3-5-fold variance reduction. An equal-weights ablation confirms that biological priors specifically contribute stability: removing priors yields statistically indistinguishable mean AUROC (p = 0.405) but 2.3x higher variance (CV 0.110 vs 0.050). Negative control experiments using permuted labels produce AUROC near or below chance (0.357 for REEF, 0.238 for NVFlare), consistent with the absence of gross data leakage. These results motivate design principles for VFL in extreme P >> N regimes, emphasizing domain-informed dimensionality reduction, stability-focused evaluation, and interpretable feature selection for scarce biological data.

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Sam Victor. 2025-12-31. Domain-aware priors stabilize, not merely enable, vertical federated learning in data-scarce coral multi-omics. https://arxiv.org/abs/2601.00050

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